NM_000249.4(MLH1):c.69del (p.Val24fs) AND Colorectal cancer, hereditary nonpolyposis, type 2

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 10, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003454188.1

Allele description [Variation Report for NM_000249.4(MLH1):c.69del (p.Val24fs)]

NM_000249.4(MLH1):c.69del (p.Val24fs)

Gene:

MLH1:mutL homolog 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

3p22.2

Genomic location:

Preferred name:

NM_000249.4(MLH1):c.69del (p.Val24fs)

HGVS:

NC_000003.12:g.36993616del
NG_007109.2:g.5267del
NG_008418.1:g.4690del
NG_099042.1:g.9del
NM_000249.4:c.69delMANE SELECT
NM_001167617.3:c.-448del
NM_001167618.3:c.-877del
NM_001167619.3:c.-790del
NM_001258271.2:c.69del
NM_001258273.2:c.-564del
NM_001258274.3:c.-1027del
NM_001354615.2:c.-558del
NM_001354616.2:c.-558del
NM_001354617.2:c.-650del
NM_001354618.2:c.-882del
NM_001354619.2:c.-1006del
NM_001354620.2:c.-216del
NM_001354621.2:c.-975del
NM_001354622.2:c.-1088del
NM_001354623.2:c.-997del
NM_001354624.2:c.-758del
NM_001354625.2:c.-656del
NM_001354626.2:c.-753del
NM_001354627.2:c.-985del
NM_001354628.2:c.69del
NM_001354629.2:c.69del
NM_001354630.2:c.69del
NP_000240.1:p.Val24Leufs
NP_000240.1:p.Val24fs
NP_001245200.1:p.Val24fs
NP_001341557.1:p.Val24fs
NP_001341558.1:p.Val24fs
NP_001341559.1:p.Val24fs
LRG_216t1:c.69del
LRG_216:g.5267del
LRG_216p1:p.Val24Leufs
NC_000003.11:g.37035106del
NC_000003.11:g.37035107del
NM_000249.3:c.69delA

Protein change:

V24fs

Molecular consequence:

NM_001167617.3:c.-448del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167618.3:c.-877del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167619.3:c.-790del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258273.2:c.-564del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258274.3:c.-1027del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354615.2:c.-558del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354616.2:c.-558del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354617.2:c.-650del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354618.2:c.-882del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354619.2:c.-1006del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354620.2:c.-216del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354621.2:c.-975del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354622.2:c.-1088del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354623.2:c.-997del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354624.2:c.-758del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354625.2:c.-656del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354626.2:c.-753del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354627.2:c.-985del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000249.4:c.69del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001258271.2:c.69del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354628.2:c.69del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354629.2:c.69del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354630.2:c.69del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Colorectal cancer, hereditary nonpolyposis, type 2 (LYNCH2)
Synonyms:: COLON CANCER, FAMILIAL NONPOLYPOSIS, TYPE 2; Lynch syndrome II; MLH1-Related Lynch Syndrome; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0012249; MedGen: C1333991; Orphanet: 144; OMIM: 609310

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004186512	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Pathogenic (Jul 10, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004186512

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))

Pathogenic
(Jul 10, 2023)

unknown

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Myriad Genetics, Inc., SCV004186512.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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